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Search results for bioinformatics transcriptomics

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51 search results found

Scanpy ⭐ 1,753

Single-cell analysis in Python. Scales to >1M cells.

Anndata ⭐ 495

Annotated data.

Pydeseq2 ⭐ 470

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Single cell perturbation prediction

R package for analyzing single-cell RNA-seq data

Diffxpy ⭐ 157

Differential expression analysis for single-cell RNA-seq data.

Pandora ⭐ 127

PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Rnalysis ⭐ 114

RNA sequencing analysis software

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Honeybadger ⭐ 94

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

just annotate it, dammit!

Singlecellhaystack ⭐ 68

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Tomicsvis ⭐ 50

Transcriptomics Visualization R package.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Metaomgraph ⭐ 30

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Volcano3d ⭐ 28

An R package to plot interactive three-way differential expression analysis

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Mudskipper ⭐ 25

A tool for projecting genomic alignments to transcriptomic coordinates

Chromoformer ⭐ 24

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

ASAP : Automated Single-cell Analysis Pipeline

Gssplayground ⭐ 21

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

(formerly eelpond) an automated RNA-Seq workflow system

Cellenium ⭐ 20

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Clustermap ⭐ 18

ClusterMap for multi-scale clustering analysis of spatial gene expression

Isotools ⭐ 15

IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.

Gene-level general linear mixed model

Gene-level general linear mixed model

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

Compbio Gists ⭐ 12

Computational Biology & Bioinformatics Resources

BACNET is a Java based platform to develop website for multi-omics analysis

Circompara ⭐ 12

🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

piano - An R/Bioconductor package for gene set analysis

Bioinformatics ⭐ 10

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Pymultiomics ⭐ 9

Python toolbox for multi-omics data mapping and analysis

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

An R wrapper for the Gemma RESTful API

Genestructuretools ⭐ 7

Glue Genes ⭐ 7

glue for genomics and transcriptomics

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Drugfindr ⭐ 5

Repository holding the code for the drugfindR R package

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

Circminer ⭐ 5

A sensitive and fast tool for circular RNA detection from RNA-Seq data

Gemmaapi.r ⭐ 5

An R wrapper for Gemma's restful API (deprecated in favour of https://github.com/PavlidisLab/gemma.R supported for personal use and leftover dependencies).

Long RNA-seq analysis workflow

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1-51 of 51 search results

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